Abstract
The cAMP receptor protein (CRP) is a global regulatory protein. We evaluated the role of CRP in starvation physiology in Salmonella Typhimurium. The Δcrp mutant survived 10 days of starvation. However, in a co-culture with the wild type in nutrient-rich medium, Δcrp died within 48 h. Similar co-culture results were observed with Escherichia coli and Staphylococcus aureus. Our study showed that the Δcrp mutant was not killed by toxins and the Type IV secretion system of the WT. The possibility of viable but non-culturable cells (VBNC) was also ruled out. However, when the overall metabolism of the co-culture was slowed down (anaerobic condition, inhibition by antibiotics and low temperature) that improved the survival of Δcrp in co-culture. But one more significant observation was that the Δcrp mutant survived in nutrient-free co-culture conditions. These two observations suggest that CRP protein is essential for efficient nutrient assimilation in a competitive environment. The cells without CRP protein are unable to evaluate the energy balance within the cell, and the cell spends energy to absorb nutrients. But the wild type cell absorbs nutrients at a faster rate than Δcrp mutant. This leads to a situation wherein the Δcrp is spending energy to absorb the nutrients but is unable to compete with the wild type. This futile metabolism leads to death. Hence, this study shows that CRP is a metabolism modulator in a complex nutrient environment. This study also highlights the need for innovative growth conditions to understand the unique function of a gene.
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References
Abisado RG, Benomar S, Klaus JR et al (2018) Bacterial quorum sensing and microbial community interactions. Mbio. https://doi.org/10.1128/mBio.02331-17
Balsalobre C, Johansson J, Uhlin BE (2006) Cyclic AMP-dependent osmoregulation of crp gene expression in Escherichia coli. J Bacteriol 188(16):5935–5944. https://doi.org/10.1128/JB.00235-06
Botsford JL, Harman JG (1992) Cyclic AMP in prokaryotes. Microbiol Rev 56:100–122. https://doi.org/10.1128/mmbr.56.1.100-122.1992
Brückner R, Titgemeyer F (2002) Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol Lett 209:141–148. https://doi.org/10.1016/S0378-1097(02)00559-1
Deutscher J (2008) The mechanisms of carbon catabolite repression in bacteria. Curr Opin Microbiol 11:87–93. https://doi.org/10.1016/j.mib.2008.02.007
Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4:457–469. https://doi.org/10.1038/nrg1088
Finkel SE (2006) Long-term survival during stationary phase: Evolution and the GASP phenotype. Nat Rev Microbiol 4:113–120. https://doi.org/10.1038/nrmicro1340
Franchini AG, Ihssen J, Egli T (2015) Effect of global regulators RpoS and cyclic-AMP/CRP on the catabolome and transcriptome of Escherichia coli K12 during carbon- and energy-limited growth. PLoS ONE. https://doi.org/10.1371/journal.pone.0133793
Gao CH, Cao H, Cai P et al (2020) The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity. ISME J 15(1):29–40. https://doi.org/10.1038/s41396-020-00751-7
Ge C, Yu Z, Sheng H et al (2022) Redesigning regulatory components of quorum-sensing system for diverse metabolic control. Nat Commun. https://doi.org/10.1038/s41467-022-29933-x
Gonzalez D, Mavridou DAI (2019) Making the best of aggression: the many dimensions of bacterial toxin regulation. Trends Microbiol 27(11):897–905. https://doi.org/10.1016/j.tim.2019.05.009
Gosset G, Zhang Z, Nayyar et al (2004) Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli. J Bacteriol 186(11):3516–3524. https://doi.org/10.1128/JB.186.11.3516-3524.2004
Gutnick D, Calvo JM, Klopotowski T et al (1969) Compounds which serve as the sole source of carbon or nitrogen for Salmonella typhimurium LT-2. J Bacteriol 100(1):215–2199. https://doi.org/10.1128/JB.100.1.215-219.1969
Ha JH, Hauk P, Cho K et al (2018) Evidence of link between quorum sensing and sugar metabolism in Escherichia coli revealed via cocrystal structures of LsrK and HPr. Sci Adv. https://doi.org/10.1126/sciadv.aar7063
Hibbing ME, Fuqua C, Parsek MR et al (2010) Bacterial competition: Surviving and thriving in the microbial jungle. Nat Rev Microbiol 8(1):15–25. https://doi.org/10.1038/nrmicro2259
Hutchison CA, Chuang RY, Noskov VN et al (2016) Design and synthesis of a minimal bacterial genome. Science. https://doi.org/10.1126/science.aad6253
Jiang C, Cheng Y, Cao H et al (2020) Effect of cAMP receptor protein gene on growth characteristics and stress resistance of haemophilus parasuis serovar 5. Front Cell Infect Microbiol 25(10):19. https://doi.org/10.3389/fcimb.2020.00019
Kendall MM, Sperandio V (2014) Cell-to-Cell Signaling in Escherichia coli and Salmonella. EcoSal plus 6(1):10. https://doi.org/10.1128/ecosalplus.esp-0002-2013
Kochanowski K, Okano H, Patsalo V et al (2021) Global coordination of metabolic pathways in Escherichia coli by active and passive regulation. Mol Syst Biol 17:4
Kolb A, Busby S, Buc H et al (1993) Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62(1):749–795. https://doi.org/10.1146/annurev.biochem.62.1.749
Lauritsen I, Frendorf PO, Capucci S, Heyde SAH, Blomquist SD, Wendel S, Fischer EC, Sekowska A, Danchin A, Nørholm MHH (2021) Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors. Nat Commun 12(1):5880. https://doi.org/10.1038/s41467-021-26098-x
Lenski RE (2017) Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations. ISME J 11(10):2181–2194. https://doi.org/10.1038/ismej.2017.69
Li YH, Tian X (2012) Quorum sensing and bacterial social interactions in biofilms. Sensors 12(3):2519–2538. https://doi.org/10.3390/s120302519
Magasanik B (2000) Global regulation of gene expression. Proc Natl Acad Sci 97(26):14044–14045. https://doi.org/10.1073/pnas.97.26.14044
Mao XJ, Huo YX, Buck M et al (2007) Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli. Nucleic Acids Res 35(5):1432–1440. https://doi.org/10.1093/nar/gkl1142
Nikhil KC, Noatia L, Priyadarsini S et al (2022) Recoding anaerobic regulator fnr of Salmonella Typhimurium attenuates it’s pathogenicity. Microb Pathog. https://doi.org/10.1016/j.micpath.2022.105591
Padan E, Bibi E, Ito M et al (2005) Alkaline pH homeostasis in bacteria: New insights. Biochim Biophys Acta Biomembr 1717(2):67–88. https://doi.org/10.1016/j.bbamem.2005.09.010
Pal A, Iyer MS, Srinivasan S et al (2022) Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology. Open Biol. https://doi.org/10.1098/rsob.210206
Paliy O, Gunasekera TS (2006) Growth of E. coli BL21 in minimal media with different gluconeogenic carbon sources and salt contents. Appl Microbiol Biotechnol. https://doi.org/10.1007/s00253-006-0554-8
Paquette SJ, Zaheer R, Stanford K et al (2018) Competition among Escherichia coli strains for space and resources. Vet Sci 5(4):93. https://doi.org/10.3390/vetsci5040093
Pinto D, Santos MA, Chambel L (2015) Thirty years of viable but nonculturable state research: Unsolved molecular mechanisms. Crit Rev Microbiol 41(1):61–76. https://doi.org/10.3109/1040841X.2013.794127
Pissaridou P, Allsopp LP, Wettstadt S et al (2018) The Pseudomonas aeruginosa T6SS-VgrG1b spike is topped by a PAAR protein eliciting DNA damage to bacterial competitors. Proc Natl Acad Sci 115(49):12519–12524. https://doi.org/10.1073/pnas.1814181115
Pope CF, McHugh TD, Gillespie SH (2010) Methods to determine fitness in bacteria. Methods Mol Biol 642:113–121. https://doi.org/10.1007/978-1-60327-279-7_9
Samhita L, Nanjundiah V, Varshney U (2014) How many initiator tRNA genes does Escherichia coli need? J Bacteriol 196(14):2607–2615. https://doi.org/10.1128/JB.01620-14
Sawant K, Shashidhar, (2020) Role of cAMP receptor protein in phenotype and stress tolerance in Salmonella enterica serovar Typhimurium. J Basic Microbiol 60(10):894–904. https://doi.org/10.1002/jobm.201900599
Sezonov G, Joseleau-Petit D, D’Ari R (2007) Escherichia coli physiology in Luria-Bertani broth. J Bacteriol 189(23):8746–8749. https://doi.org/10.1128/JB.01368-07
Sgro GG, Oka GU, Souza DP et al (2019) Bacteria-Killing Type IV Secretion Systems. Front Microbiol 10:1078. https://doi.org/10.3389/fmicb.2019.01078
Shimada T, Fujita N, Yamamoto K (2011) Novel roles of camp receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS ONE. https://doi.org/10.1371/journal.pone.0020081
Singh KD, Schmalisch MH, Stülke J et al (2008) Carbon catabolite repression in Bacillus subtilis: Quantitative analysis of repression exerted by different carbon sources. J Bacteriol 190(21):7275–7284. https://doi.org/10.1128/JB.00848-08
van Tatenhove-Pel RJ, Rijavec T, Lapanje A et al (2020) Microbial competition reduces metabolic interaction distances to the low µm-range. ISME J. https://doi.org/10.1038/s41396-020-00806-9
Wiser MJ, Lenski RE (2015) A comparison of methods to measure fitness in Escherichia coli. PLoS ONE. https://doi.org/10.1371/journal.pone.0126210
Yang Z, Li Q, Yan Y et al (2021) Master regulator NtrC controls the utilization of alternative nitrogen sources in Pseudomonas stutzeri A1501. World J Microbiol Biotechnol 37(10):177. https://doi.org/10.1007/s11274-021-03144-w
Yong YC, Zhong JJ (2013) Impacts of quorum sensing on microbial metabolism and human health. Adv Biochem Eng Biotechnol 131:25–61. https://doi.org/10.1007/10_2012_138
Zambrano MM, Siegele DA, Almirón M et al (1993) Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 259(5102):1757–1760. https://doi.org/10.1126/science.7681219
Zhang Z, Ren Q (2015) Why are essential genes essential?: the essentiality of Saccharomyces genes. Microb Cell 2(8):280–287. https://doi.org/10.15698/mic2015.08.218
Zheng D, Constantinidou C, Hobman JL et al (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res 32(19):5874–5893. https://doi.org/10.1093/nar/gkh908
Acknowledgements
We thank the Department of Atomic Energy, Government of India, for financial support. We acknowledge Dr Shridhar Paranjape and Dr Sahayog Jamdar for the discussions related to the experimental set-up.
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This work was supported by the Department of Atomic Energy, Government of India, for financial support.
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Ms.S carried out all the experiments and interpretation of results. Mr. R.S carried out the conceptualization of the study, result interpretation and manuscript writing. Both the authors have read and approved the final manuscript.
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Sawant, K., Shashidhar, R. The cAMP receptor protein (CRP) enhances the competitive nature of Salmonella Typhimurium. Arch Microbiol 205, 197 (2023). https://doi.org/10.1007/s00203-023-03528-6
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DOI: https://doi.org/10.1007/s00203-023-03528-6